RetrogeneDB ID: retro_eeur_603

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_359993:6303..6762(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000014488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSEEUG00000002419
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_eeur_603
TGTCCCTCTTCCAGTGGAAAGCCCAACCATGCAGACATCTTGCTCATAAATTTACAGTATGTTTCAGAAGTGGAAATTAT
TAATGACCGAACGGAAACCCCTCCTCCCCTAGCTTCACTCAATGTTAGTAAGCTTGCCAGCAAAGCACGGACAGAGAAGG
AGGAGAAGCTGAGCCAGGCCTATGCAATCAGCGCCGGTGTCTCCCTTGAGGGCCAGCAGCTTTTCCAGACCATTCACAAG
ACCATTAAAGATTGTAAATGGCAAGAAAAGAACATTGTAGTCATGGAAGAAGTTGTTATTACACCCCCATATCAAGTGGA
AAACTGTAAAGGCAAAGAGGGGAGTGCACTGAGCCATGTACGAAAAATAGTTGAAAAACATTTTAGAGACGTGGAAAGCC
AAAAGATAATGCAGCGTTCACAAGCCCAGCAACCACAGAAGGAGGCTGCTCTGTCATCC

Alignment

ORF - retro_eeur_603 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLE
          CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLE
Retrocopy CPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLE

Parental  GQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVESLKIMQRS
          GQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVES.KIMQRS
Retrocopy GQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVESQKIMQRS

Parental  QAQQPQKEAALSS
          QAQQPQKEAALSS
Retrocopy QAQQPQKEAALSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	11.44 RPM	2.58 RPM
SRP017611_kidney	9.00 RPM	3.94 RPM
SRP017611_liver	11.09 RPM	1.61 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_603 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603 ,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,